PDBsum entry 4xo0

Transferase/DNA

PDB id: 4xo0

Contents

Protein chain

248 a.a.

DNA/RNA

Waters ×201

PDB id:

4xo0

Name:

Transferase/DNA

Title:

Crystal structure of 5'-cttatpptazzataag in a host-guest complex

Structure:

Reverse transcriptase. Chain: a. Fragment: unp residues 683-937. Synonym: pr180gag-pol. Engineered: yes. DNA (5'-d( Cp Tp Tp Ap Tp (1Wa)p (1Wa)p T)-3'). Chain: b. Engineered: yes. DNA (5'-d(p Ap (1W5)p (1W5)p Ap Tp Ap Ap G)-3').

Source:

Moloney murine leukemia virus (isolate shinnick). Momlv. Organism_taxid: 928306. Strain: isolate shinnick. Gene: gag-pol. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes.

Resolution:

1.70Å R-factor: 0.221 R-free: 0.241

Authors:

M.M.Georgiadis,I.Singh

Key ref:

M.M.Georgiadis et al. (2015). Structural basis for a six nucleotide genetic alphabet. J Am Chem Soc, 137, 6947-6955. PubMed id: 25961938

Date:

16-Jan-15 Release date: 27-May-15

Protein chain

P03355  (POL_MLVMS) -  Gag-Pol polyprotein from Moloney murine leukemia virus (isolate Shinnick)

Seq: 1738 a.a.

Struc: 248 a.a.

DNA/RNA chains

C-T-T-A-T-1WA-1WA-T 8 bases

A-1W5-1W5-A-T-A-A-G 8 bases

Enzyme reactions

• Enzyme class 2: E.C.2.7.7.- - ?????
• Enzyme class 3: E.C.2.7.7.49 - RNA-directed Dna polymerase.
• Reaction: DNA(n) + a 2'-deoxyribonucleoside 5'-triphosphate = DNA(n+1) + diphosphate
• Enzyme class 4: E.C.2.7.7.7 - DNA-directed Dna polymerase.
• Reaction: DNA(n) + a 2'-deoxyribonucleoside 5'-triphosphate = DNA(n+1) + diphosphate
• Enzyme class 5: E.C.3.1.-.-
• Enzyme class 6: E.C.3.1.26.4 - ribonuclease H.
• Reaction: Endonucleolytic cleavage to 5'-phosphomonoester.
• Enzyme class 7: E.C.3.4.23.- - ?????

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

J Am Chem Soc 137:6947-6955 (2015)

PubMed id: 25961938

Structural basis for a six nucleotide genetic alphabet.

M.M.Georgiadis, I.Singh, W.F.Kellett, S.Hoshika, S.A.Benner, N.G.Richards.

ABSTRACT

Expanded genetic systems are most likely to work with natural enzymes if the added nucleotides pair with geometries that are similar to those displayed by standard duplex DNA. Here, we present crystal structures of 16-mer duplexes showing this to be the case with two nonstandard nucleobases (Z, 6-amino-5-nitro-2(1H)-pyridone and P, 2-amino-imidazo[1,2-a]-1,3,5-triazin-4(8H)one) that were designed to form a Z:P pair with a standard "edge on" Watson-Crick geometry, but joined by rearranged hydrogen bond donor and acceptor groups. One duplex, with four Z:P pairs, was crystallized with a reverse transcriptase host and adopts primarily a B-form. Another contained six consecutive Z:P pairs; it crystallized without a host in an A-form. In both structures, Z:P pairs fit canonical nucleobase hydrogen-bonding parameters and known DNA helical forms. Unique features include stacking of the nitro group on Z with the adjacent nucleobase ring in the A-form duplex. In both B- and A-duplexes, major groove widths for the Z:P pairs are approximately 1 Å wider than those of comparable G:C pairs, perhaps to accommodate the large nitro group on Z. Otherwise, ZP-rich DNA had many of the same properties as CG-rich DNA, a conclusion supported by circular dichroism studies in solution. The ability of standard duplexes to accommodate multiple and consecutive Z:P pairs is consistent with the ability of natural polymerases to biosynthesize those pairs. This, in turn, implies that the GACTZP synthetic genetic system can explore the entire expanded sequence space that additional nucleotides create, a major step forward in this area of synthetic biology.